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Tracking down ammonites in the Denver, Colorado, area

In July 2013, I visited the Denver, Colorado, area to collect data from two collections housed at United States Geological Survey (USGS) facilities and the University of Colorado (CU) Museum of Natural History. The USGS collections are housed in the Core Research Center on the Denver Federal Center campus. The building is also a repository for a large collection of soil samples and approximately 1.7 million feet of drilled rock, sediment, and ice cores. The Museum of Natural History is located at the University of Colorado campus in scenic Boulder, Colorado.

Though these collections cover a wide range of organisms from all over the world, my purpose there was to visit the fossil collections from the Western Interior Seaway. The Western Interior Seaway was a widespread shallow sea that flooded the North American continent from the Gulf of Mexico to the Arctic Ocean during the Late Cretaceous Period (about 100 to 65 million years ago). My work focuses on the faunal dynamics associated with invasion into these shallow sea environments. By more closely examining natural experiments in the past when biota encountered widespread novel physical conditions, we can better inform our predictions of how organisms will respond to the rapid global change happening today.

To that extent, I was interested in photographing and documenting a portion of the vast numbers of ammonites the two institutions have amassed over the years. Ammonites are a completely extinct group of hard-shelled cephalopods, related to the modern-day squid, octopus, and nautilus. Their fossils are often sold in rock shops because their beautiful undulating suture lines make them aesthetically pleasing items. They were incredibly diverse and abundant during the time the Western Interior Seaway existed, and so are an ideal study group to explore the dynamics of this system.

Acanthoceras sp.

An Acanthoceras sp. specimen (UCM11843) collected from the Lower Cretaceous rocks in Colorado, now housed at the CU Museum of Natural History.

The large collection of Cretaceous bivalves, gastropods, and ammonites kept in the USGS collection is primarily the result of work done by USGS geologists, such as William Cobban, who collected and published on the Western Interior throughout the late 20th century and is still at the USGS facilities in Denver today. The collection contains drawer upon drawer of specimens. With the generous help of curator Kevin “Casey” McKinney, I photographed hundreds of ammonites, including many unpublished specimens. These photographs will be used to identify morphological features that may have influenced the degree to which ammonites were able to invade or adapt to the seaway. It was an adventure exploring the dusty cabinets, where every drawer held a surprise.

Drawer of ammonites

A drawer filled with nothing but ammonites at the USGS facilities.

After four days in the suburbs of Denver, I took a bus up to beautiful Boulder, Colorado, just 45 minutes outside of Denver proper. After winding my way through the University of Colorado-Boulder campus, I arrived at the Bruce Curtis Building where the museum collections were housed. Collection manager Talia Karim greeted me and helped me get set up before showing me around the collections housed in the basement. Here, there were not as many specimens as at the USGS, but they were no less impressive. During the next three days, I photographed about a hundred more beautifully prepared specimens before I had to say goodbye to the Denver area.

The richness of the collections were such that, no matter how often I visit, there will always be much more to discover. I have plans to return in the near future to continue my explorations of these amazing and underused resources.

Examining morphologic variation in varanid skulls through time and space

As a graduate student affiliated with the UCMP, there are many resources readily available to me. Not only does the museum have the largest university research collection, but the curators, museum scientists, and staff are some of the most knowledgeable and helpful anywhere. UCMP is recognized for taking care of its graduate students, and one of the ways they do it is by providing multiple funding opportunities. I applied to UCMP for funding last year in order to conduct museum travel for my research and I was fortunate to get an award from the Welles Fund.

One major aspect of my research focuses on looking at shape differences in the skulls of monitor lizards. Monitor lizards, or varanids, are generally thought of as being fairly large lizards (e.g., Komodo dragon), but some may be no longer than a pencil. Although there are many extinct species and genera within this group, there are approximately 70 living species in the single genus Varanus. They live in Africa, Southern Asia, and Australia, and are ecologically versatile, with some being strictly terrestrial, arboreal, or even semi-aquatic. Fossil varanids from Asia may be as much as 90 million years old; varanid fossils are also found in North America and Europe.

Two varanids

Left: A Komodo dragon (Varanus komodoensis) from the Cincinnati Zoo. Photo by Mark Dumont (CC BY 2.0). Right: The smallest monitor lizard, a neonate Varanus brevicauda. Photo courtesy of Eric R. Pianka.

Thanks to my Welles Fund award, last year I was able to visit the American Museum of Natural History in New York, The Yale Peabody Museum in New Haven, CT, and the Australian Museum in Sydney, Australia. At these museums I photographed the skulls of over 300 modern varanid skulls, getting top, side, and bottom views of each. I use these photos for a technique called Geometric Morphometrics. Morphometrics (greek “morphe” or shape, and “metria” or measurement) is a general term used for describing the quantification of shape. Many fields within biology use this technique to study numerous questions, like changes from juvenile to adult morphologies, how ecology influences shape, and in my case, comparing species from different regions to each other and to those in the fossil record. Geometric Morphometrics is a technique that uses landmarks (coordinates) placed on photos of specimens that can be regarded as a a similar point in each specimen in the study. There are various ways of analyzing the data, but essentially the locations of the landmarks on different specimens are compared and quantified. One main analysis conducted with this data is called Principal Component Analysis which tells you where the maximum amount of variation in your specimens happens to be. This allows the researcher to determine how much shape difference exists in their specimens of interest. In my case, museum visits are essential since they allow for adequate sample sizes to compare the species found in different locations of this group.

Varanid skull

Example of a Varanus skull with landmarks. Photo of AMNH specimen by Elizabeth Ferrer.

I was able to analyze the data to answer various questions, and one of the most interesting discoveries was that the varanids in Africa, where there are only about six species, are almost as morphologically variable as those in, for example, Australia where there are approximately 30 species (depending on where you designate certain groups). I am continuing to analyze and collect data, but I am thankful to the UCMP for providing the finanical assistance necessary for me to complete a large portion of my dissertation project. As a side benefit, traveling to distant museums allowed me to visit interesting and beautiful locations!

Freemantle Beach and Sydney Opera House

Fremantle Beach, Western Australia (left), and Sydney Opera House, Sydney, Australia (right). Photos by Elizabeth Ferrer.

California pollen taphonomy and pollen trap study in Clear Lake, California

Pollen analysis (or palynology) has been used to study Quaternary changes in vegetation and climate in North America since the nineteenth century. Palynologists generally compare plant assemblages in spatial-time frames instead of focusing on particular plant species. These changes in plant assemblages across landscapes through time are a good indication of vegetation shifts caused by environmental changes. Besides using pollen assemblages to reconstruct parent plant communities in a particular area, certain species, which are sensitive to changes in temperature or precipitation, are of special interest. By comparing assemblages of plant communities and these indicative species through time and space, we can infer how regional flora responded to environmental changes such as changes in climate.

Before comparing these past assemblages of plant communities and inferring environmental changes, palynologists carefully consider the processes leading to pollen accumulation. Do their pollen and spore assemblages accurately reflect local or more regional vegetation? Are certain pollen types over- or underrepresented? Does the assemblage include the majority of taxa present in the local plant communities? Pollen assemblages are incorporated in sediments at the end of a long taphonomic pathway, and are affected by temporal and quantitative aspects of pollen and spore production, differential dispersal characteristics, secondary transport, and other taphonomic processes.

How could we get hints of that process throughout geologic time? Wind-pollinated assemblages are most often transported and they are usually produced in large amounts and have wider dispersal ranges. To study the taphonomic process of pollen and spores, palynologists often use surface samples to research the discrepancy between vegetation composition and pollen assemblages. Such analysis also might help to understand the taphonomic conditions in the sample area and provide a reference point for a regional paleopalynological study.

First version of pollen trap

First version of a modified Olefield pollen trap (Jantz et al. 2013).

For my dissertation research, I am compiling a California pollen reference collection. Focused on the last interglacial period, I plan to reconstruct the vegetation from a relatively warm period during that time interval. My methods involve extracting pollen from core samples from Clear Lake. Clear Lake is the largest lake in California with a sedimentary record going back at least to the last interglacial period (~130 ka) (see Scientists core into Clear Lake to explore past climate change). The microscopic pollen grains are expected to yield important clues on the history of vegetation communities and the taphonomic process surrounding Clear Lake; data from pollen traps set in different vegetation areas in the vicinity of the lake — forests up to 2 km from the lake, or small, more distant upstream communities — will enable further analysis of modern vegetation types.

The most common pollen in Clear Lake samples is wind-pollinated, mostly pine and oak pollen. An important question is: does this pollen mainly originate from the northwestern forests, the southwestern forests, or other adjacent places? To solve this question, I started to look for appropriate types of pollen traps to collect surface samples and, with the help of my undergrads, Mary Grace Rodriguez and Rebecca Shirsat, we built some traps to position in the field.

After visiting the Clear Lake area a couple of times, I positioned the first 10 pollen traps close to the lake — many thanks to Carolyn Ruttan from Lake County Water Resources who helped me obtain landowners' permits for this.

The first time doing field research is often filled with anticipation. On January 20, I left Berkeley in the early morning. I was so excited — not only because I could finally install my pollen traps, but because it would be only my second time driving through winding mountain roads!

After meeting Carolyn Ruttan I set off to Clear Lake State Park, our first pollen trap site. I selected a rocky corner of the lake that had a gorgeous view. Securing this first pollen trap to the ground was a challenge, but we stabllized the base with pebbles and used a small iron wire to prevent the trap from blowing over in the wind.

The next trap was easier to position, being on soft soil in Anderson Marsh. We only had to avoid picking a spot where weeds might cover the area later in the year.

The Lake County Land Trust’s Rodman Preserve is another one of my research sites. The trust was formed as a non-profit organization in 1994 and it works to protect important land resources, wetlands, forests, etc., in Lake County, CA.

Preparing to install a trap and one in the Rodman Preserve

Left: Preparing to install pollen traps in Clear Lake State Park. Right: Pollen trap in the Lake County Land Trust's Rodman Preserve.

The Elem Indian Colony, near Clearlake Oaks on the eastern shore of Clear Lake, is my fourth research site. It is a Native American colony of Pomo, associated with the Sulphur Bank Rancheria. The residents were friendly and curious about our purpose. I am sure they will help prevent tourists from removing the trap that we placed near a power station.

We then attached pollen traps to railings and floating platforms at three sites. Installation of the first 10 pollen traps was completed on this first trip; we went back two weeks later to complete the west side of the lake.

Pollen traps on platforms

Two pollen traps attached to floating platforms.

The most serious threat to my traps is the strong winds around Clear Lake, especially on the northwest side. Strong, seasonal winds can take down deeply-rooted trees and it could damage the pollen traps. Squirrels and birds might also be a problem but hopefully, the iron wires we used will keep them safe from animals. I plan to return to Clear Lake later in the year to replace trap materials and to see what my pollen traps have collected (if the squirrels and birds have not absconded with my trap materials)!

The hunt for a Ph.D. thesis: Collecting Late Cretaceous plant fossils in New Mexico

"It ain't Mexico and it ain't new" [quoted from a postcard in a gift shop]

Armed with hammers, chisels, pry-bars, boxes of newspaper, and sunscreen, two trusty assistants (recent graduate Meriel Melendrez and current undergrad Nicolas Locatelli) and I drove from Berkeley in our 4WD extra-long SUV heading for southern New Mexico. There, we met up with paleobotanist Dr. Gary Upchurch and crew from Texas State University and geologist Dr. Greg Mack from New Mexico State University for two weeks of field work in Late Cretaceous plant localities of the Jose Creek Member. It was a bona fide tri-state expedition working on multiple projects. My interests were to set the foundation for my dissertation work on the ecological diversity of Late Cretaceous forests in warm-wet climates. For this I needed a primary study site to generate new collections and data. The trip wasn’t entirely exploratory — I was familiar with some of the localities from my undergraduate days with Dr. Upchurch, and had collected here previously. Based on this earlier work, we knew that there was an abundance of plant fossils, and preliminary studies have indicated that the fossil assemblages of the Jose Creek Member represent a subtropical-paratropical forest. That’s right, in the present day desert of New Mexico, rich in angiosperms but mixed with conifers and ferns.

Late Cretaceous plant communities often contain interesting combinations of plants that are no longer found living together under the same climatic conditions (for example palms and redwoods). That is because the Late Cretaceous represents an important transitional time, as flowering plants (angiosperms) rapidly diversified and rose to dominance in warmer climates. During this time, the typical early to mid-Mesozoic forests that were dominated by ferns and gymnosperms (conifers and other non-flowering seed plants) transitioned to the modern, angiosperm-dominated forests. This begs several questions: what were the different ecological roles of angiosperms and conifers in these forests, and did conifers and other gymnosperms serve functions that have now been replaced by angiosperms? How has the structure of plant communities in warm-wet climates changed from the Cretaceous to present, and how does this inform our understanding of the evolution of modern tropical forests? These are the questions that fueled my quest into the southwest last summer. The New Mexico sites seemed like an ideal place to start my investigations, and we ambitiously set out to do some major collecting.

In the Jose Creek Member, the best-preserved plant fossils come from beds of recrystallized volcanic ash. My initial goal was to collect quadrats from multiple volcanic ash beds, which would give an indication of the vegetation through time (because beds are not necessarily deposited at the exact same time). But things don’t always work out like you plan, and luckily this was one of those times ….

Field site

Field site on the distant hills (can you see the exposure?), but with modern vegetation of course! Photo by Meriel Melendrez.

Dori with palm frond

Fossil palm frond (with Dori for scale). Photo by Meriel Melendrez.

Preparing a collecting site

Meriel and Nick preparing a collecting site. Photo by Dori Contreras.

The first locality we went to had an ash bed that was known for its abundance of plant fossils and beautiful preservation. After setting up the first collecting quadrat with Meriel and Nicolas, Dr. Mack and I headed off to investigate how far we could track the exposed bed, as its lateral extent was hitherto unknown. To our amazement, we were able to track the deposit for ~1.2 km! This was an incredible revelation; here were the remains of a forest preserved in ash for quite an impressive spatial extent, which would enable the reconstruction of a plant community at a single instant in time. This was considerably more attractive for my questions than reconstructing vegetation from multiple beds comprising an unknown amount of geologic time. I adjusted plans and concentrated our efforts on this deposit alone (rather than a compilation of sites) and spent the next nine days collecting small quadrats along the length of the bed. The deposit is so rich that virtually every rock we cracked open had multiple fossil plant specimens! Consequently, almost everything we touched was wrapped in newspaper, hiked out of the field site, and brought back to the UCMP. This was no light task — thank goodness for the incredible Meriel and Nicolas! In total we collected samples from 14 sites along the exposure. These initial collections reveal a rich and laterally diverse flora, and yet are only the tip of the iceberg!

We headed back west with the SUV packed to the brim and riding low from the weight of the fossils; it was the maximum that could possibly be brought back. I should also mention — Cindy Looy and Ivo Duijnstee, along with some of the other Looy Lab members (Jeff, Renske, Robert) — were in New Mexico for a conference and we arranged to meet them. This was particularly fortuitous, not only for good company, but also because they took two large tubs of fossils back with them! Another two tubs went back to Texas, and made it to Berkeley later that summer. All in all, it was enough fossils to fill two double-door cases in the museum!

Of course, the field work is only the beginning and, since then, a lot of work has gone into getting these first collections organized and examined. Currently, two students (James Buckel and Negin Sarrami) and I are describing and photographing leaf morphotypes from the collections to assess the diversity of plants in the flora. A large portion probably represent unknown/undescribed species, so we differentiate ‘species’ as morphotypes based on detailed descriptions of leaf characteristics. The flora includes a diversity of herbaceous and woody ‘dicots’, monocots (e.g., palms and ginger), cycads, ferns, an abundant extinct sequoia-like conifer and several extinct conifers probably related to the Araucariaceae. Overall, it is clear that it will take several more field excursions and countless hours of lab work to understand the taxonomic and structural diversity of this amazing flora. And, of course, I am eagerly looking forward to the return trips and uncovering the treasure trove of fossils still entombed in the rock out in the desert!

Fossil fern

Fossil fern. Photo by Dori Contreras.

Angiosperm leaf

Angiosperm leaf with insect feeding damage (holes). Photo by Dori Contreras.

Waterlogged wood on the seafloor and the critters that call it home

For a marine biologist, I spend a lot of time thinking about wood. What happens to it if it happens to wash into a stream? How much of it gets into the ocean? Where does it sink? What happens to it once it reaches the bottom? What animals are likely to make it their home?

I’m far from the first to think about the role of wood in ocean systems. In fact, Darwin thought quite a bit about how plant material might make its way into the ocean and how long different kinds of wood might stay afloat before sinking …

“It is well known what a difference there is in the buoyancy of green and seasoned timber; and it occurred to me that floods might wash down plants or branches, and that these might be dried on the banks, and then by a fresh rise in the stream be washed into the sea. Hence I was led to dry stems and branches of 94 plants with ripe fruit, and to place them on sea water. The majority sank quickly, but some which whilst green floated for a very short time, when dried floated much longer ….”
— Darwin, excerpted from On the Origin of Species, Chapter 11, 1859.

While Darwin’s focus was on wood as a rafting vehicle for dispersal, I am interested in the flip side: what happens to that wood once it sinks (where it is no longer useful for transporting land-dwelling animals)? Is the wood very useful to certain specialized denizens of the deep? Like Darwin, I recognized that there may be different effects depending on what kind of wood is involved, therefore, I set out to test whether the kind of wood matters in shaping the community of animals that colonize it.

About two and a half years ago, I had an opportunity to sink material from ten very different plants with support from Jim Barry and his lab at the Monterey Bay Aquarium Research Institute (MBARI). We took the research vessel Western Flyer to a site about a day's steam from Moss Landing, CA, and with help from the remotely operated vehicle Doc Ricketts, we placed 28 wood bundles on the seafloor about two miles below the surface.

Processing wood and extracting clams

Left: On board the Western Flyer, Jenna and Rosemary Romero process wood after it was brought up from the seafloor. Right: Connie Martin carefully extracts clams from a chunk of Ginkgo wood.

For two years I waited, not knowing whether I would ever see my beloved wood bundles again. But thanks to the expertise of my colleagues and good weather, I was able to retrieve every single wood bundle last October.

Since then, the lab has been quite the scene with six — yes, I said six — undergraduate research assistants busily extracting animals from the inside of logs and off the surface of leaves and needles. Each of them has developed an eye for detail that only hours upon hours of sorting tiny animals under the microscope can give you. Together we are sorting through heaps of critters and pulling out the patterns that make each colonist community different on each type of wood. Already patterns are emerging, but it will take more sorting, photographing and identifying organisms with help from taxonomist colleagues at other museums and institutions before we have the full story. Please stay tuned!

Christopher Castaneda sorts critters

Christopher Castaneda sorts critters and records his observations.

Learn more about this research in an interview that aired on the radio talk show The Graduates with Tesla Monson on KALX, April 22, 2014. You can download the audio podcast on iTunes.

Links to related articles and posts:

— This research was funded in part by the UCMP, Sigma Xi Berkeley Chapter, Conchologists of America, AMNH Lerner-Gray, and American Malacological Society. The wood used in this research was collected from a variety of sources, including the Tilden Botanical Garden, City of Berkeley, UC Berkeley campus, and other helpful businesses and individuals.

Grad student's artwork graces journal cover

“There are great color reconstructions of dinosaurs, so why not a plant?” thought Department of Integrative Biology and UCMP grad student Jeff Benca when he set out to reconstruct the appearance of a 375-million-year-old Devonian plant. Using Adobe Illustrator CS6 software, he constructed a striking three-dimensional, full-color portrait of a stem of the lycopod Leclercqia scolopendra, or centipede clubmoss. This was no small feat, considering that the fossil plant Jeff was illustrating was a two-dimensional compression.

Jeff Benca and journal cover

Left: Jeff Benca with museum visitors on Cal Day 2014. Photo by Pat Holroyd. Right: Jeff's artwork on the cover of the March 2014 issue of the American Journal of Botany.

The illustration appears in a paper by Jeff and coauthors Maureen Carlisle, Silas Bergen, and UCMP alum Caroline Strömberg in the March 2014 issue of the American Journal of Botany. Jeff’s illustration graces the cover of the issue (see photo above).

Read more about Jeff and his work with fossil and living lycopods at the UC Berkeley Newscenter. Read the abstract for the paper, "Applying morphometrics to early land plant systematics: A new Leclercqia (Lycopsida) species from Washington State, USA."

Following The Graduates on KALX Berkeley

Tesla at the microphone

Tesla Monson, KALX radio talk show host.

UCMP and Department of Integrative Biology graduate student Tesla Monson, a second-year graduate student in the Hlusko Lab, is the host of a new talk show, The Graduates, on KALX Berkeley,! KALX is a UC Berkeley and listener-supported independent radio station and an ideal platform for The Graduates, a show featuring Tesla interviewing UCB graduate students about their research. Debuting on Tuesday, April 8, at 9:00am, The Graduates will air every other Tuesday, from 9:00 am to 9:30 am on KALX Berkeley, 90.7 FM.

Tesla’s first two interview subjects are UCMP graduate students. On April 8, Ashley Poust will discuss dinosaurs and early mammals, and on April 22, Jenna Judge will talk about deep-sea marine biology. Stay tuned!

Audio podcasts of all The Graduates interviews are available on iTunes.

The geology and paleontology of the Caldecott Tunnel's Fourth Bore

Tunnel cross-sectionThe fourth bore of the Caldecott Tunnel opened to traffic on November 16, 2013, and if you're an East Bay resident, chances are good that you've been through it once or twice (at least!). Did you realize that each time you drive through the tunnel you're passing through several million years of accumulated sediment that has been pushed up on its side?

Want to know more about the rocks the tunnel cuts through and the fossils found in them? As part of an agreement between UCMP and the California Department of Transportation (Caltrans), the museum has created a web-based feature focusing on the geology and paleontology of the tunnel's fourth bore. The feature covers …

… the tectonic history of the East Bay

… the geology of the East Bay Hills

… the preparations taken prior to excavation of the fourth bore

… the method and sequence of excavation

… and the fossils that have been prepared and cataloged (so far).

Erica, PaleoPortal, and the National Fossil Day connection

Erica working on an exhibit

Erica working on an exhibit at the Glen Canyon National Recreation Area. Photo courtesy of the National Park Service.

Before coming to UCMP, Erica Clites — currently working on an NSF-funded project to rehouse and digitally image the orphaned USGS Menlo Park invertebrate collection out at the Regatta facility in Richmond — spent about two and a half years with the National Park Service. In 2010 she coordinated a nationwide outreach effort for the first NPS-sponsored National Fossil Day, which was held on October 16th this year. Read an interview with Erica about her work with the NPS on the Park Service's National Fossil Day website.

While at the NPS, Erica worked with Vince Santucci of the NPS Geologic Resources Division. At the same time, Vince was helping UCMP with its "Fossils in US National Parks" module on The Paleontology Portal website; he provided much of the park and fossil data necessary to create the module, which, by the way, was made in support of National Fossil Day.

Who lived here before the Giants?

For the third consecutive year, UCMP participated in the Bay Area Science Festival at AT&T Park as one of several Science@Cal exhibitors. The November 2, 2013, festival drew more than 28,000 science fans and Lisa White, Tripti Bhattacharya, and volunteer CJ Dunford staffed a UCMP table. With a theme of "Who lived here before the Giants?," the UCMP fossil display and activities were a big hit with the little fans!

BASF photos

Left: A young scientist examines a fossil oyster. Right: Staffing the UCMP table are (from left) Tripti Bhattacharya, CJ Dunford, and Lisa White.